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Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [RNA-seq]

ABSTRACT: Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [RNA-seq]

OTHER RELATED OMICS DATASETS IN: GSE109955GSE109903GSE109954

PROVIDER: PRJNA432416 | ENA |

REPOSITORIES: ENA

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Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [WES]

Project description:Whole exome sequencing of matched patient-derived xenograft in vitro-in vivo models.

2018-01-31 | GSE109954 | GEO

Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [RNA-seq]

Project description:Transcriptome levels of matched patient-derived xenograft (PDX) in vitro-in vivo models.

2018-01-31 | GSE109903 | GEO

Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer

Project description:Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer

| PRJNA432411 | ENA

Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [WES]

Project description:Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [WES]

| PRJNA432417 | ENA

Gene expression profile at single cell level of matched primary tumor and metastatic cells of breast cancer patient-derived xenograft models

Project description:We profiled the tumor heterogeneity of individual primary tumor and matched metastatic cells of breast cancer using a set of patient derived xenograft models with different metastatic potentials. This data set gives insights into the transcriptional tumor heterogeneity, the transcriptional differences between primary tumor and matched metastatic cells and how these are changing in regard to varying metastatic phenotypes.

2022-08-15 | GSE211146 | GEO

Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-01-31 | GSE109955 | GEO

Transcriptomic analysis of patient-derived ex vivo models of pancreatic cancer

Project description:The aim of this study is to compare the transcriptomic profiles of various ex vivo models of pancreatic cancer. First, primary tumours and their corresponding xenografts in nude mice were analysed by RNA-seq. Monocultures of pancreatic cancer cells derived from the xenografts were then prepared as 2D monolayers, Matrigel-embedded organoids, spheres in suspension and 3D cultures in self-assembling peptide amphiphile (PA) hydrogels. Seven-day cultures were then analysed by RNA-seq. The results suggest that all ex vivo monocultures retain patient-specific transcriptional profiles, especially cancer stem cell signatures, while being deficient in the expression of stromal components such as the core matrisome. Correlations with the primary tumours were generally higher in PA hydrogels than organoids. Biased gene expression signatures were identified in certain models. This is the first study to explore the transcriptomic signatures of four different ex vivo models matched to their primary tumours of origin.

2021-07-03 | GSE139184 | GEO

RNA-seq of human mesenchymal stromal cells cultured in PEG hydrogels with and without FGF-2

Project description:FGF-2 is commonly used in culture media when growing mechenchymal stromal cells. Here, we cultured human MSCs from 3 donors with and without 50 ng/ml FGF-2 (Prepotech, human recombinant) in 3D PEG hydrogels, and analysed transcriptome changes by RNA sequencing.

2020-06-02 | E-MTAB-8510 | biostudies-arrayexpress

Carboplatin resistance-associated changes in the 3D chromatin landscape of a triple-negative breast cancer Patient-Derived Xenograft [RNA-Seq]

Project description:Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. However, little is known about the rewiring of the 3D chromatin landscape during cancer progression to a chemotherapy-resistant state. We utilized a patient-derived xenograft (PDX) mouse model of triple-negative breast cancer (UCD52) to characterize changes in the 3D structure between the primary tumor and carboplatin-resistant state. Systematic integration of matched chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing data revealed a widespread increase in short-range (<2Mb) interactions with the corresponding increase in chromatin looping and topologically associating domain (TAD) formation, chromatin state switching into a more active state, large-scale deletions, amplification of ATP-binding cassette (ABC) transporters and nearly complete shutdown of drug metabolism pathways. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of many aggressiveness-, metastasis- and other cancer-related pathways. Transcriptome changes suggest the role of downregulated protein-coding genes and upregulated long-noncoding RNAs in drug resistance. Integrative analysis confirmed increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial metabolic processes. Our results highlight that 3D genome remodeling may be a key mechanism underlying drug resistance.

2023-04-06 | GSE201434 | GEO